The dead included 10 men and six women, the Malaysian Maritime Enforcement Agency (MMEA) said in a statement.
Fourteen people were found safe, while 20 remain missing, as search and rescue operations continued for a second day.
All those aboard the boat, which overturned off Malaysia's southern Johor state in bad weather on Wednesday, were Indonesians suspected to be undocumented migrants travelling to Malaysia, the MMEA has said.
The accident is the latest in a string of disasters recorded in the waterways between Indonesia and Malaysia in recent years, often involving overloaded boats ferrying labourers seeking work in Malaysian factories and plantations.
According to Jakarta-based rights group Migrant CARE, between 100,000 and 200,000 Indonesians travel illegally to Malaysia each year for work, many of them recruited by trafficking gangs.